This is kind of tied in with my last post about the necessary usb booting files. Since some of them can't be removed, and those that can still leave like 10 files cluttering up the drive's root, I have found (by rtfm) that syslinux.cfg and its required files can be moved to its own folder.

So move everything except Knoppix/Knoppix to a folder called /syslinux, or /boot/syslinux.